[BioPython] genbank annotation

Hi!
I have two genbank genome files, one of the old kind where each region is
noted twize, and one where they are unique.
What I would like to extract from this is the feature information, in
this sort of format:
Type start stop direction name
In the first case, where almost all regions are noted twize, I'd like
to have only one of them included in the list.
You have a genbank parser thing in biopython which I'd like to use,
however, I cannot figure out how to use it to do this.
The files:
The first:
source 1..2944528
/organism="Listeria monocytogenes"
/mol_type="genomic DNA"
/strain="EGD-e"
/db_xref="taxon:1639"
gene 305..1673
/gene="dnaA"
RBS 305..310
CDS 318..1673
/codon_start=1

[BioPython] Is BioPython thread safe?

Brandon King <kingb <at> caltech.edu>
2004-10-11 23:04:53 GMT

Hi All,
I'm trying to use BioPython within a thread of my main program and I
end up getting this error. Is BioPython intended to be thread safe?
TraceBack:
<snip>
from Bio.Blast import NCBIStandalone
File "/usr/lib/python2.3/site-packages/Bio/__init__.py", line 106, in ?
_load_registries()
File "/usr/lib/python2.3/site-packages/Bio/__init__.py", line 98, in
_load_registries
module = __import__("Bio.config.%s" % module, {}, {}, ["Bio","config"])
File "/usr/lib/python2.3/site-packages/Bio/config/FormatRegistry.py",
line 26, in ?
import _support
File "/usr/lib/python2.3/site-packages/Bio/config/_support.py", line
26, in ?
from Bio.MultiProc.copen import copen_fn
File "/usr/lib/python2.3/site-packages/Bio/MultiProc/copen.py", line
322, in ? signal.signal(signal.SIGTERM, _handle_sigterm)
ValueError: signal only works in main thread
-Brandon King
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[BioPython] regular expression and filtering dna strings

enrico curiotto <curienri <at> yahoo.com>
2004-10-12 10:52:41 GMT

Hello everybody,
I have the following problem:
A have a series of strings, some of them are DNA strings (so they
contain only ACGT), other not.
How can I filter out not DNA strings?
Maybe this can be properly done quickly with regular expression
in python, without using biopython.
Does anyone know how to do that with regular expression ?
Thank you very much,
Enrico.
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Re: [BioPython] regular expression and filtering dna strings

Hi Enrico,
If your DNA strings never contain anything other than ACGT, then a
result other than 'None' for re.search('[^ACGT]', your_string) will be
diagnostic for non-DNA sequences. A None result will not, however, be
diagnostic for DNA...
Python 2.3.2 (#1, Dec 12 2003, 11:27:04)
[GCC 3.3.2 20031022 (Red Hat Linux 3.3.2-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
|>> import re
|>> a = 'ACGTGTACGT'
|>> b = 'ACAGFTAGAT'
|>> re.search('[^ACGT]', a)
|>> print re.search('[^ACGT]', a)
None
|>> print re.search('[^ACGT]', b)
<_sre.SRE_Match object at 0xbf511368>
HTH,
enrico curiotto wrote:
| Hello everybody,
| I have the following problem:
| A have a series of strings, some of them are DNA strings (so they
| contain only ACGT), other not.
| How can I filter out not DNA strings?
| Maybe this can be properly done quickly with regular expression
| in python, without using biopython.

[BioPython] Transplanting Biopython to a live file system

Sebastian Bassi <sbassi <at> asalup.org>
2004-10-14 16:17:57 GMT

Hello all,
I did copy Bio, mx and Numeric from a working linux installation to
another (under Site-Packages). Then I tried to "import Bio" from the new
system and I got there is no module named Bio.
I know this not a kosher way to install Biopython, but I have to do it
this way to make it available on DNALinux that it is a liveCD (a working
linux system from CD, like Knoppix).
Do you may know what went wrong?
I think I solved something like this 2 month ago when I transplanted
Biopython to the AMD64 (because it didnt compile on AMD64, so I
transplanted) and it worked. But this time, it doesnt :(
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[BioPython] flatfile index using OBDA registry system and biopython

Siddhartha Basu <basu <at> pharm.sunysb.edu>
2004-10-14 19:03:44 GMT

Hi,
I have just started using biopython and wants to use OBDA registry
system to index the swissprot flat files. My goal is to access and make
indexed file using different language. I already searched through the
biopython docs but couldn't really figure out how to call the registry
system from biopython. I have already setup a a seqdatabase.ini file,
now to use that from biopython.
Any idea, help will be highly appreciated.
Thanks in advance,
Siddhartha
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